Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view preclassification.xml @ 6:3c50a937d7c1 draft
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author | bcclaywell |
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date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | d4690e65afcd |
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<tool id="PHYLO_preclassification" name="Generate database" version="1.2.0"> <description>for classification</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> <stdio> <expand macro="basic_errors"/> </stdio> <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> preclassification-wrapper.sh ${config} </command> <inputs> <param name="dedup_info" type="data" format="csv" label="Deduplication info"/> <param name="refpkg" type="data" format="refpkg" label="Reference package"/> <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/> <param name="placed_seqs" type="data" format="jplace" label="Placements"/> </inputs> <outputs> <data name="reduped_seqs" format="jplace" label="Reduped placements"/> <data name="class_db" format="sqlite3" label="Placement database"/> </outputs> <configfiles> <configfile name="config"> DEDUP_INFO="${dedup_info}" REFPKG="${refpkg.extra_files_path}" NBC_SEQS="${nbc_seqs}" PLACED_SEQS="${placed_seqs}" REDUPED_SEQS="${reduped_seqs}" CLASS_DB="${class_db}" </configfile> </configfiles> <!-- The contents of the help tag is parsed as reStructuredText. Please see help-template.rst for examples of commonly-used sections in other Galaxy tools. --> <help> .. class:: infomark **What it does** This tool outputs the classifications made by ``pplacer`` to a database for use in taxonomic classification. </help> <citations> <expand macro="cite_pplacer"/> </citations> </tool>